Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.54, per 1000 atoms: 0.46 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 129.9 milliseconds Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 596 0.92 - 1.17: 1062 1.17 - 1.42: 635 1.42 - 1.67: 824 1.67 - 1.92: 36 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.456 1.697 -0.241 1.16e-02 7.43e+03 4.32e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.680 -0.222 1.18e-02 7.18e+03 3.55e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.025 0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta sigma weight residual 1.459 1.231 0.227 1.28e-02 6.10e+03 3.15e+02 bond pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 1.522 1.308 0.214 1.26e-02 6.30e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 3141 4.52 - 9.04: 1848 9.04 - 13.56: 658 13.56 - 18.08: 115 18.08 - 22.61: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BLYS A 93 " pdb=" C BLYS A 93 " pdb=" N BGLU A 94 " ideal model delta sigma weight residual 122.03 106.01 16.02 1.04e+00 9.25e-01 2.37e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 105.70 13.50 9.00e-01 1.23e+00 2.25e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.27 140.62 -18.35 1.23e+00 6.61e-01 2.23e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 131.52 -12.89 9.20e-01 1.18e+00 1.96e+02 angle pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 121.41 106.99 14.42 1.04e+00 9.25e-01 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 16.93: 932 16.93 - 33.84: 123 33.84 - 50.74: 39 50.74 - 67.64: 14 67.64 - 84.55: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N THR A 160 " pdb=" CA THR A 160 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 126 0.270 - 0.541: 72 0.541 - 0.811: 33 0.811 - 1.081: 10 1.081 - 1.352: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 123 " pdb=" CA VAL A 123 " pdb=" CG1 VAL A 123 " pdb=" CG2 VAL A 123 " both_signs ideal model delta sigma weight residual False -2.63 -1.28 -1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CA ALA A 39 " pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CB ALA A 39 " both_signs ideal model delta sigma weight residual False 2.48 1.40 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.118 2.00e-02 2.50e+03 7.01e-02 1.48e+02 pdb=" CG PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.022 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.082 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.201 9.50e-02 1.11e+02 9.12e-02 9.07e+01 pdb=" NE ARG A 48 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.089 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 736 2.27 - 2.86: 7847 2.86 - 3.44: 10631 3.44 - 4.02: 15351 4.02 - 4.60: 22092 Nonbonded interactions: 56657 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.693 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.775 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.804 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.829 1.850 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.836 1.850 ... (remaining 56652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_2780949_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.798304 | | target function (ml) not normalized (work): 233115.507787 | | target function (ml) not normalized (free): 11853.557220 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3049 0.2067 7.0677 4.9451| | 2: 3.57 - 2.84 1.00 2876 122 0.2434 0.1854 4.3509 4.3393| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1667 4.1281 4.1628| | 4: 2.47 - 2.25 1.00 2825 136 0.2354 0.1388 3.8332 3.8188| | 5: 2.25 - 2.09 1.00 2756 127 0.2467 0.1568 3.7996 3.8258| | 6: 2.09 - 1.97 1.00 2846 113 0.2535 0.1793 3.4696 3.5412| | 7: 1.97 - 1.87 1.00 2787 165 0.2533 0.1950 3.1475 3.2211| | 8: 1.87 - 1.79 1.00 2789 144 0.2495 0.1982 3.0853 3.159| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1952 2.9262 2.9834| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.2150 2.8306 2.9304| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.2006 2.7586 2.7875| | 12: 1.61 - 1.56 1.00 2787 146 0.2514 0.2084 2.632 2.7252| | 13: 1.56 - 1.52 1.00 2745 130 0.2637 0.1827 2.6197 2.5656| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1953 2.5296 2.5853| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.2114 2.4256 2.5162| | 16: 1.45 - 1.42 1.00 2756 161 0.2626 0.2177 2.3801 2.426| | 17: 1.42 - 1.39 1.00 2785 139 0.2641 0.2174 2.3305 2.3929| | 18: 1.39 - 1.36 1.00 2741 179 0.2639 0.2116 2.2666 2.2686| | 19: 1.36 - 1.34 1.00 2807 134 0.2664 0.2225 2.2403 2.2281| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2060 2.1936 2.1268| | 21: 1.32 - 1.30 1.00 2785 112 0.2675 0.1973 2.1694 2.0926| | 22: 1.29 - 1.27 1.00 2704 152 0.2749 0.2505 2.1461 2.2172| | 23: 1.27 - 1.26 1.00 2802 156 0.2846 0.2608 2.1242 2.2062| | 24: 1.26 - 1.24 1.00 2744 132 0.2742 0.2834 2.0815 2.2604| | 25: 1.24 - 1.22 1.00 2734 148 0.2848 0.2711 2.0521 2.1222| | 26: 1.22 - 1.21 1.00 2727 135 0.2849 0.2457 2.0029 2.1135| | 27: 1.21 - 1.19 1.00 2814 148 0.2932 0.2544 2.004 2.0227| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2702 1.9927 1.9714| | 29: 1.18 - 1.16 1.00 2800 134 0.2999 0.2774 1.9717 2.0477| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.2912 1.9332 2.0145| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.84 0.76 0.23 1471.93| | 2: 3.57 - 2.84 2876 122 0.80 25.97 1.27 0.23 1471.93| | 3: 2.84 - 2.48 2833 165 0.74 31.92 1.24 0.23 1221.77| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 572.58| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 572.58| | 6: 2.09 - 1.97 2846 113 0.83 22.89 1.29 0.25 315.76| | 7: 1.97 - 1.87 2787 165 0.89 17.18 1.28 0.26 96.74| | 8: 1.87 - 1.79 2789 144 0.85 21.73 1.25 0.26 96.74| | 9: 1.79 - 1.72 2745 138 0.87 19.12 1.23 0.26 59.06| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.26 51.51| | 11: 1.66 - 1.61 2740 147 0.85 21.99 1.24 0.26 49.69| | 12: 1.61 - 1.56 2787 146 0.88 18.90 1.23 0.25 31.21| | 13: 1.56 - 1.52 2745 130 0.86 20.96 1.24 0.25 31.21| | 14: 1.52 - 1.48 2803 134 0.86 20.98 1.23 0.25 27.61| | 15: 1.48 - 1.45 2738 128 0.87 20.46 1.24 0.25 21.02| | 16: 1.45 - 1.42 2756 161 0.85 21.75 1.23 0.25 21.02| | 17: 1.42 - 1.39 2785 139 0.87 20.34 1.23 0.25 17.35| | 18: 1.39 - 1.36 2741 179 0.87 20.56 1.22 0.25 15.22| | 19: 1.36 - 1.34 2807 134 0.86 21.48 1.22 0.25 15.22| | 20: 1.34 - 1.32 2696 147 0.87 20.34 1.21 0.25 12.51| | 21: 1.32 - 1.30 2785 112 0.86 21.42 1.19 0.25 12.32| | 22: 1.29 - 1.27 2704 152 0.86 21.82 1.21 0.24 12.14| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.22 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 22.92 1.19 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 24.10 1.21 0.24 10.86| | 26: 1.22 - 1.21 2727 135 0.83 24.71 1.20 0.23 10.41| | 27: 1.21 - 1.19 2814 148 0.83 25.38 1.20 0.23 10.41| | 28: 1.19 - 1.18 2671 147 0.82 25.97 1.19 0.23 9.70| | 29: 1.18 - 1.16 2800 134 0.82 26.09 1.16 0.23 9.43| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.15 0.23 9.43| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.43 max = 1471.93 mean = 215.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.79| |phase err.(test): min = 0.00 max = 89.16 mean = 22.81| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.241 1557 Z= 5.541 Angle : 5.357 19.115 2118 Z= 3.758 Chirality : 0.407 1.352 243 Planarity : 0.033 0.084 284 Dihedral : 14.093 84.545 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.48), residues: 224 helix: -2.56 (0.41), residues: 102 sheet: -1.40 (0.82), residues: 28 loop : -0.45 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.021 ARG A 98 TYR 0.090 0.046 TYR A 141 PHE 0.105 0.036 PHE A 164 HIS 0.038 0.019 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.798304 | | target function (ml) not normalized (work): 233115.507787 | | target function (ml) not normalized (free): 11853.557220 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2612 0.1964 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2612 0.1964 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1988 0.1964 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2010 0.2014 0.1981 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1774 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1774 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3836 386.343 358.939 0.723 0.929 0.409 11.894-9.307 99.02 97 4 0.1806 613.686 593.589 1.001 0.930 0.390 9.237-7.194 100.00 213 7 0.2152 501.920 491.585 1.034 0.930 0.354 7.162-5.571 100.00 427 22 0.2205 376.663 364.240 1.002 0.930 0.299 5.546-4.326 100.00 867 58 0.1247 517.065 511.249 1.044 0.930 0.225 4.315-3.360 100.00 1859 96 0.1143 491.733 487.874 1.082 0.930 0.143 3.356-2.611 100.00 3867 181 0.1445 323.043 320.093 1.074 0.930 0.099 2.608-2.026 99.99 8198 413 0.1367 214.148 211.605 1.084 0.929 0.000 2.025-1.573 100.00 17313 902 0.1653 104.579 103.863 1.088 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2085 46.374 45.025 1.078 0.927 0.000 1.221-1.150 99.97 13689 708 0.2592 29.219 26.973 1.051 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0484 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1644 r_free=0.1774 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.923514 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.376711 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1695 0.1813 0.0118 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1560 0.1703 0.0143 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1464 0.1635 0.0170 0.001 0.4 3.8 0.0 0.0 0 0.500 0.1377 0.1569 0.0192 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1552 0.0198 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1362 0.1564 0.0202 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1291 0.1511 0.0220 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1268 0.1499 0.0231 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1257 0.1493 0.0236 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1244 0.1478 0.0234 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1240 0.1481 0.0241 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1478 0.0240 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1233 0.1474 0.0242 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1471 0.0240 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1227 0.1473 0.0246 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1224 0.1473 0.0249 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1222 0.1475 0.0253 0.007 0.9 4.2 0.5 0.0 0 12.962 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1471 0.0240 0.006 0.8 4.2 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.71 2.40 3.013 19.070 1992.377 0.017 12.31 14.71 2.39 2.977 19.070 59.771 0.017 12.37 14.69 2.32 2.668 19.068 249.047 0.017 12.77 15.47 2.70 3.056 19.433 996.188 0.017 12.54 15.48 2.94 3.061 19.461 1992.377 0.016 12.45 15.50 3.05 3.315 19.638 2988.565 0.015 12.36 15.50 3.14 3.410 19.675 3984.753 0.015 12.32 15.50 3.18 3.403 19.659 4980.942 0.015 12.25 15.44 3.20 3.448 19.687 5977.130 0.015 12.24 15.47 3.22 3.278 19.579 6973.318 0.015 12.19 15.42 3.22 3.220 19.530 7969.507 0.015 12.19 15.46 3.27 3.442 19.651 8965.695 0.015 12.16 15.47 3.31 3.500 19.667 9961.884 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 249.047 Accepted refinement result: 12.37 14.69 2.32 2.668 19.068 249.047 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.09 3.31 0 1785 Protein: 9.08 115.01 17.00 3.32 0 1519 Water: 11.47 119.46 38.24 N/A 0 258 Other: 19.69 26.62 22.07 N/A 0 8 Chain A: 9.08 119.46 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1469 r_work=0.1239 r_free=0.1473 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1473 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016992 | | target function (ls_wunit_k1) not normalized (work): 1415.422330 | | target function (ls_wunit_k1) not normalized (free): 110.012434 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1467 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1694 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1232 0.1459 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1232 0.1459 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3552 301.674 281.632 0.651 1.003 0.380 11.894-9.307 99.02 97 4 0.1631 483.264 471.993 0.923 1.003 0.369 9.237-7.194 100.00 213 7 0.1908 395.251 388.862 0.964 1.003 0.344 7.162-5.571 100.00 427 22 0.1832 296.614 290.543 0.937 1.003 0.259 5.546-4.326 100.00 867 58 0.1003 407.177 404.410 0.964 1.003 0.199 4.315-3.360 100.00 1859 96 0.0877 387.229 386.070 1.007 1.002 0.170 3.356-2.611 100.00 3867 181 0.1181 254.389 253.266 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.1027 168.637 167.908 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.353 82.524 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.519 36.022 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 23.009 21.485 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1459 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1233 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1459 | n_water=258 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1243 r_free=0.1460 | n_water=250 | time (s): 21.730 (total time: 23.870) Filter (q & B) r_work=0.1245 r_free=0.1460 | n_water=247 | time (s): 3.200 (total time: 27.070) Compute maps r_work=0.1245 r_free=0.1460 | n_water=247 | time (s): 1.260 (total time: 28.330) Filter (map) r_work=0.1259 r_free=0.1454 | n_water=225 | time (s): 3.160 (total time: 31.490) Find peaks r_work=0.1259 r_free=0.1454 | n_water=225 | time (s): 0.460 (total time: 31.950) Add new water r_work=0.1398 r_free=0.1612 | n_water=435 | time (s): 2.320 (total time: 34.270) Refine new water occ: r_work=0.1301 r_free=0.1478 adp: r_work=0.1226 r_free=0.1434 occ: r_work=0.1239 r_free=0.1424 adp: r_work=0.1207 r_free=0.1414 occ: r_work=0.1210 r_free=0.1404 adp: r_work=0.1199 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1402 r_work=0.1199 r_free=0.1402 | n_water=435 | time (s): 54.860 (total time: 89.130) Filter (q & B) r_work=0.1204 r_free=0.1405 | n_water=420 | time (s): 3.360 (total time: 92.490) Filter (dist only) r_work=0.1204 r_free=0.1404 | n_water=419 | time (s): 33.110 (total time: 125.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.364701 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.088187 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1685 0.1793 0.0108 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1566 0.1686 0.0120 0.001 0.4 8.3 0.0 0.0 0 0.250 0.1421 0.1564 0.0143 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1343 0.1504 0.0161 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1317 0.1485 0.0168 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1321 0.1490 0.0168 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1260 0.1452 0.0192 0.002 0.5 5.4 0.5 0.0 0 2.000 0.1225 0.1422 0.0197 0.003 0.6 5.8 0.5 0.0 0 3.000 0.1216 0.1429 0.0213 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1208 0.1415 0.0207 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1204 0.1420 0.0216 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1201 0.1418 0.0217 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1196 0.1412 0.0217 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1192 0.1414 0.0221 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1191 0.1416 0.0225 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1189 0.1410 0.0221 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1188 0.1416 0.0228 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1182 0.1413 0.0231 0.008 0.9 5.1 0.5 0.0 0 13.682 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1410 0.0221 0.007 0.9 4.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 14.10 2.21 3.777 21.774 1483.088 0.016 11.89 14.10 2.21 3.777 21.774 44.493 0.016 11.89 14.10 2.21 3.777 21.774 185.386 0.016 12.10 14.54 2.44 3.620 21.786 741.544 0.015 12.07 14.83 2.76 3.449 22.045 1483.088 0.015 11.93 14.81 2.87 3.445 22.121 2224.632 0.014 11.83 14.74 2.91 3.477 22.146 2966.176 0.014 11.75 14.77 3.02 3.514 21.957 3707.720 0.014 11.77 14.86 3.09 3.502 22.201 4449.265 0.014 11.71 14.79 3.07 3.508 22.194 5190.809 0.014 11.71 14.84 3.12 3.521 22.146 5932.353 0.014 11.67 14.82 3.15 3.533 22.127 6673.897 0.014 11.67 14.87 3.19 3.550 22.165 7415.441 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.493 Accepted refinement result: 11.89 14.10 2.21 3.777 21.774 44.493 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.17 3.31 194 1752 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.71 40.80 N/A 194 225 Other: 19.73 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.45 N/A 0 1752 Chain S: 14.49 60.00 46.78 N/A 194 0 Histogram: Values Number of atoms 9.11 - 19.71 1260 19.71 - 30.30 247 30.30 - 40.89 161 40.89 - 51.49 136 51.49 - 62.08 120 62.08 - 72.67 11 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1410 r_work=0.1189 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1410 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014892 | | target function (ls_wunit_k1) not normalized (work): 1240.466665 | | target function (ls_wunit_k1) not normalized (free): 103.482681 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1410 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1586 0.1584 0.1640 n_refl.: 87592 remove outliers: r(all,work,free)=0.1586 0.1584 0.1640 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1587 0.1585 0.1641 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1186 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1195 0.1185 0.1402 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3339 300.221 274.026 0.599 1.003 0.350 11.894-9.307 99.02 97 4 0.1510 483.264 479.297 0.928 1.003 0.330 9.237-7.194 100.00 213 7 0.1608 395.251 398.076 0.988 1.003 0.280 7.162-5.571 100.00 427 22 0.1560 296.614 292.666 0.933 1.003 0.224 5.546-4.326 100.00 867 58 0.0876 407.177 403.910 0.961 1.003 0.189 4.315-3.360 100.00 1859 96 0.0785 387.229 386.217 1.004 1.002 0.170 3.356-2.611 100.00 3867 181 0.1098 254.389 253.317 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1018 168.637 168.051 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1098 82.353 82.586 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.519 36.051 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.009 21.518 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0093 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1402 | n_water=419 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1185 r_free=0.1400 | n_water=416 | time (s): 34.140 (total time: 36.400) Filter (q & B) r_work=0.1185 r_free=0.1400 | n_water=416 | time (s): 0.970 (total time: 37.370) Compute maps r_work=0.1185 r_free=0.1400 | n_water=416 | time (s): 1.740 (total time: 39.110) Filter (map) r_work=0.1230 r_free=0.1385 | n_water=283 | time (s): 3.190 (total time: 42.300) Find peaks r_work=0.1230 r_free=0.1385 | n_water=283 | time (s): 0.480 (total time: 42.780) Add new water r_work=0.1340 r_free=0.1510 | n_water=461 | time (s): 2.360 (total time: 45.140) Refine new water occ: r_work=0.1247 r_free=0.1428 adp: r_work=0.1249 r_free=0.1429 occ: r_work=0.1224 r_free=0.1410 adp: r_work=0.1224 r_free=0.1409 occ: r_work=0.1206 r_free=0.1403 adp: r_work=0.1202 r_free=0.1398 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1398 r_work=0.1202 r_free=0.1398 | n_water=461 | time (s): 198.110 (total time: 243.250) Filter (q & B) r_work=0.1206 r_free=0.1404 | n_water=433 | time (s): 2.940 (total time: 246.190) Filter (dist only) r_work=0.1206 r_free=0.1403 | n_water=431 | time (s): 34.270 (total time: 280.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.811917 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.863476 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1241 0.1372 0.0130 0.002 0.6 6.4 0.5 0.0 0 0.091 0.1192 0.1341 0.0149 0.003 0.7 5.4 0.5 0.0 0 0.272 0.1176 0.1334 0.0158 0.004 0.8 5.1 0.5 0.0 0 0.544 0.1169 0.1332 0.0163 0.005 0.9 5.1 0.5 0.0 0 0.815 0.1166 0.1330 0.0165 0.006 1.0 4.8 0.5 0.0 0 1.087 0.1162 0.1332 0.0170 0.007 1.0 5.4 0.5 0.0 0 1.359 0.1160 0.1332 0.0172 0.007 1.1 5.4 0.5 0.0 0 1.631 0.1158 0.1332 0.0174 0.008 1.1 5.8 0.5 0.0 0 1.903 0.1167 0.1331 0.0164 0.006 0.9 5.4 0.5 0.0 0 0.906 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1330 0.0165 0.006 1.0 4.8 0.5 0.0 0 1.087 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 13.30 1.65 3.780 21.213 42.863 3.627 11.66 13.30 1.65 3.780 21.213 1.286 3.627 11.66 13.31 1.64 3.768 21.213 5.358 3.627 11.74 13.41 1.68 3.709 21.201 21.432 3.622 11.74 13.50 1.76 3.730 21.176 42.863 3.622 11.67 13.47 1.80 3.754 21.164 64.295 3.616 11.60 13.43 1.83 3.771 21.159 85.727 3.610 11.55 13.38 1.83 3.778 21.159 107.159 3.607 11.57 13.46 1.89 3.799 21.140 128.590 3.607 11.53 13.43 1.90 3.808 21.141 150.022 3.605 11.52 13.42 1.90 3.820 21.135 171.454 3.604 11.50 13.41 1.90 3.826 21.134 192.886 3.602 11.52 13.44 1.92 3.842 21.127 214.317 3.602 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.286 Accepted refinement result: 11.66 13.30 1.65 3.780 21.213 1.286 3.627 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.14 3.31 210 1748 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.51 76.71 35.58 N/A 210 221 Other: 19.73 26.66 22.11 N/A 0 8 Chain A: 9.12 115.05 19.39 N/A 0 1748 Chain S: 14.49 60.01 35.72 N/A 210 0 Histogram: Values Number of atoms 9.12 - 19.71 1264 19.71 - 30.31 287 30.31 - 40.90 204 40.90 - 51.49 130 51.49 - 62.08 51 62.08 - 72.68 11 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1166 r_free=0.1330 r_work=0.1166 r_free=0.1330 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1166 r_free = 0.1330 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1336 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1156 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.620379 | | target function (ml) not normalized (work): 301555.836202 | | target function (ml) not normalized (free): 15873.943571 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1156 0.1336 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1495 0.1494 0.1558 n_refl.: 87590 remove outliers: r(all,work,free)=0.1495 0.1494 0.1558 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1493 0.1557 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1152 0.1331 n_refl.: 87590 remove outliers: r(all,work,free)=0.1157 0.1148 0.1331 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3788 294.703 268.548 0.499 1.000 0.320 11.894-9.307 97.06 95 4 0.2269 476.592 462.180 0.875 1.002 0.280 9.237-7.194 98.18 209 7 0.2287 386.717 389.697 0.957 1.002 0.203 7.162-5.571 100.00 427 22 0.2101 296.614 286.445 0.919 1.002 0.166 5.546-4.326 100.00 867 58 0.1122 407.177 402.188 0.965 1.002 0.141 4.315-3.360 100.00 1859 96 0.0953 387.229 384.436 1.004 1.002 0.123 3.356-2.611 100.00 3867 181 0.1132 254.389 252.245 1.008 1.001 0.080 2.608-2.026 99.99 8198 413 0.0939 168.637 167.776 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0905 82.353 82.622 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.519 36.088 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.009 21.535 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0132 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1331 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1148 r_free=0.1331 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1331 | n_water=431 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1148 r_free=0.1330 | n_water=430 | time (s): 44.820 (total time: 47.240) Filter (q & B) r_work=0.1148 r_free=0.1329 | n_water=426 | time (s): 3.860 (total time: 51.100) Compute maps r_work=0.1148 r_free=0.1329 | n_water=426 | time (s): 1.880 (total time: 52.980) Filter (map) r_work=0.1175 r_free=0.1305 | n_water=320 | time (s): 3.980 (total time: 56.960) Find peaks r_work=0.1175 r_free=0.1305 | n_water=320 | time (s): 0.730 (total time: 57.690) Add new water r_work=0.1242 r_free=0.1373 | n_water=478 | time (s): 3.730 (total time: 61.420) Refine new water occ: r_work=0.1173 r_free=0.1314 adp: r_work=0.1174 r_free=0.1317 occ: r_work=0.1158 r_free=0.1298 adp: r_work=0.1157 r_free=0.1300 occ: r_work=0.1147 r_free=0.1287 adp: r_work=0.1144 r_free=0.1287 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1287 r_work=0.1144 r_free=0.1287 | n_water=478 | time (s): 306.290 (total time: 367.710) Filter (q & B) r_work=0.1150 r_free=0.1291 | n_water=442 | time (s): 3.940 (total time: 371.650) Filter (dist only) r_work=0.1150 r_free=0.1291 | n_water=440 | time (s): 45.590 (total time: 417.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.786982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.371840 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1335 0.0126 0.002 0.6 6.1 0.5 0.0 0 0.089 0.1170 0.1307 0.0137 0.003 0.7 4.8 0.5 0.0 0 0.268 0.1155 0.1296 0.0141 0.005 0.9 4.8 0.5 0.0 0 0.536 0.1149 0.1293 0.0144 0.006 1.0 5.1 0.5 0.0 0 0.804 0.1143 0.1297 0.0153 0.006 1.0 4.8 0.5 0.0 0 1.072 0.1143 0.1290 0.0147 0.007 1.1 5.4 0.5 0.0 0 1.340 0.1139 0.1295 0.0156 0.008 1.1 4.5 0.5 0.0 0 1.608 0.1138 0.1291 0.0154 0.008 1.1 5.1 0.5 0.0 0 1.876 0.1147 0.1294 0.0147 0.006 1.0 4.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1290 0.0147 0.007 1.1 5.4 0.5 0.0 0 1.340 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.90 1.47 3.780 21.138 47.372 3.609 11.43 12.90 1.47 3.780 21.138 1.421 3.609 11.43 12.90 1.47 3.765 21.138 5.921 3.608 11.50 13.02 1.52 3.715 21.122 23.686 3.606 11.47 13.08 1.61 3.744 21.099 47.372 3.604 11.43 13.08 1.65 3.765 21.087 71.058 3.600 11.39 13.05 1.66 3.778 21.083 94.744 3.596 11.33 12.98 1.65 3.784 21.086 118.430 3.592 11.35 13.04 1.69 3.809 21.064 142.116 3.593 11.33 13.02 1.69 3.821 21.062 165.801 3.591 11.32 13.01 1.69 3.831 21.059 189.487 3.590 11.30 12.99 1.69 3.836 21.059 213.173 3.589 11.29 12.98 1.68 3.845 21.056 236.859 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.421 Accepted refinement result: 11.43 12.90 1.47 3.780 21.138 1.421 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.01 3.31 220 1747 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.71 34.71 N/A 220 220 Other: 19.73 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.35 N/A 0 1747 Chain S: 14.49 60.00 34.15 N/A 220 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.30 298 30.30 - 40.89 220 40.89 - 51.49 118 51.49 - 62.08 46 62.08 - 72.67 10 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1290 r_work=0.1143 r_free=0.1290 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1290 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1287 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1287 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606792 | | target function (ml) not normalized (work): 300391.692084 | | target function (ml) not normalized (free): 15820.870742 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1138 0.1287 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1472 0.1472 0.1500 n_refl.: 87581 remove outliers: r(all,work,free)=0.1472 0.1472 0.1500 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1471 0.1471 0.1499 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1290 n_refl.: 87581 remove outliers: r(all,work,free)=0.1144 0.1137 0.1290 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4003 291.324 259.442 0.452 0.999 0.286 11.894-9.307 97.06 95 4 0.2497 476.592 462.247 0.850 1.002 0.263 9.237-7.194 98.18 209 7 0.2422 386.717 381.076 0.928 1.002 0.178 7.162-5.571 100.00 427 22 0.2148 296.614 285.577 0.911 1.002 0.146 5.546-4.326 100.00 867 58 0.1160 407.177 402.218 0.965 1.002 0.121 4.315-3.360 100.00 1859 96 0.0920 387.229 385.176 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1109 254.389 252.699 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0919 168.637 167.989 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.353 82.708 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.519 36.119 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 23.009 21.548 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1290 After: r_work=0.1138 r_free=0.1290 ================================== NQH flips ================================== r_work=0.1138 r_free=0.1290 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1138 r_free=0.1290 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1290 | n_water=440 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1138 r_free=0.1290 | n_water=440 | time (s): 44.470 (total time: 46.900) Filter (q & B) r_work=0.1138 r_free=0.1290 | n_water=440 | time (s): 1.330 (total time: 48.230) Compute maps r_work=0.1138 r_free=0.1290 | n_water=440 | time (s): 1.840 (total time: 50.070) Filter (map) r_work=0.1174 r_free=0.1320 | n_water=351 | time (s): 4.200 (total time: 54.270) Find peaks r_work=0.1174 r_free=0.1320 | n_water=351 | time (s): 0.680 (total time: 54.950) Add new water r_work=0.1223 r_free=0.1370 | n_water=500 | time (s): 3.830 (total time: 58.780) Refine new water occ: r_work=0.1156 r_free=0.1301 adp: r_work=0.1156 r_free=0.1301 occ: r_work=0.1144 r_free=0.1288 adp: r_work=0.1143 r_free=0.1289 occ: r_work=0.1136 r_free=0.1282 adp: r_work=0.1133 r_free=0.1280 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1280 r_work=0.1133 r_free=0.1280 | n_water=500 | time (s): 273.670 (total time: 332.450) Filter (q & B) r_work=0.1141 r_free=0.1289 | n_water=456 | time (s): 4.050 (total time: 336.500) Filter (dist only) r_work=0.1141 r_free=0.1289 | n_water=454 | time (s): 46.780 (total time: 383.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.737069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.267727 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1345 0.0116 0.004 0.7 5.8 0.0 0.0 0 0.087 0.1175 0.1309 0.0134 0.004 0.8 5.4 0.0 0.0 0 0.261 0.1159 0.1299 0.0140 0.005 0.9 4.8 0.5 0.0 0 0.521 0.1149 0.1293 0.0144 0.006 1.0 4.5 0.5 0.0 0 0.782 0.1143 0.1290 0.0147 0.007 1.1 4.5 0.5 0.0 0 1.042 0.1141 0.1289 0.0148 0.007 1.1 4.5 0.5 0.0 0 1.303 0.1140 0.1290 0.0149 0.008 1.1 4.2 0.5 0.0 0 1.563 0.1139 0.1289 0.0150 0.008 1.1 4.5 0.5 0.0 0 1.824 0.1147 0.1292 0.0145 0.006 1.0 4.5 0.5 0.0 0 0.869 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1289 0.0150 0.008 1.1 4.5 0.5 0.0 0 1.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 12.89 1.50 3.780 21.198 44.268 3.607 11.39 12.89 1.50 3.780 21.198 1.328 3.607 11.39 12.89 1.50 3.779 21.198 5.533 3.607 11.47 12.97 1.50 3.713 21.182 22.134 3.605 11.42 12.99 1.57 3.739 21.167 44.268 3.602 11.41 13.04 1.63 3.761 21.145 66.402 3.599 11.34 12.99 1.65 3.776 21.144 88.535 3.594 11.34 12.98 1.65 3.787 21.136 110.669 3.592 11.30 12.96 1.66 3.798 21.137 132.803 3.590 11.30 12.98 1.68 3.814 21.124 154.937 3.590 11.27 12.96 1.69 3.820 21.126 177.071 3.588 11.27 12.96 1.69 3.831 21.122 199.205 3.587 11.25 12.94 1.69 3.835 21.124 221.339 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.328 Accepted refinement result: 11.39 12.89 1.50 3.780 21.198 1.328 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.12 3.31 236 1745 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 34.80 N/A 236 218 Other: 19.72 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.33 N/A 0 1745 Chain S: 14.48 60.00 34.35 N/A 236 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.30 303 30.30 - 40.89 221 40.89 - 51.48 129 51.48 - 62.07 43 62.07 - 72.67 10 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1289 r_work=0.1139 r_free=0.1289 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1289 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1288 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1137 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605869 | | target function (ml) not normalized (work): 300311.224044 | | target function (ml) not normalized (free): 15811.201296 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1362 0.1354 5.6779 5.6407| | 2: 3.57 - 2.84 1.00 2888 124 0.1064 0.1361 5.1715 5.2096| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1270 4.9546 5.0086| | 4: 2.47 - 2.25 1.00 2825 136 0.0909 0.0945 4.6405 4.6487| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0962 4.5838 4.6388| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.0996 4.274 4.3627| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1096 3.9748 4.0837| | 8: 1.87 - 1.79 1.00 2789 144 0.0913 0.1108 3.8859 3.9989| | 9: 1.79 - 1.72 1.00 2745 138 0.0866 0.1144 3.6409 3.8017| | 10: 1.72 - 1.66 1.00 2831 160 0.0915 0.1171 3.5616 3.7011| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1061 3.4915 3.5762| | 12: 1.61 - 1.56 1.00 2773 144 0.0901 0.1135 3.3283 3.4597| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1049 3.3058 3.409| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1055 3.2395 3.3223| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1196 3.1522 3.2515| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1249 3.1343 3.2445| | 17: 1.42 - 1.39 1.00 2785 139 0.1132 0.1308 3.115 3.225| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1330 3.1028 3.2333| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1565 3.1124 3.2683| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1460 3.1105 3.1527| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1506 3.1147 3.1063| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1970 3.1239 3.2892| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1804 3.1337 3.2004| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1815 3.1277 3.2192| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2146 3.1445 3.2605| | 26: 1.22 - 1.21 1.00 2727 135 0.1912 0.1770 3.1505 3.2036| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2192 3.1725 3.1691| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2296 3.1677 3.1719| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2381 3.15 3.2304| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2449 3.1441 3.1684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2922 171 0.95 8.65 1.00 0.97 5911.84| | 2: 3.57 - 2.84 2888 124 0.92 12.75 1.01 0.97 5911.84| | 3: 2.83 - 2.48 2820 163 0.89 16.69 0.99 0.97 4934.29| | 4: 2.47 - 2.25 2825 136 0.92 13.58 1.00 0.98 2413.51| | 5: 2.25 - 2.09 2756 127 0.90 15.83 1.01 0.98 2413.51| | 6: 2.09 - 1.97 2846 113 0.92 12.44 1.02 0.98 1385.89| | 7: 1.97 - 1.87 2787 165 0.95 9.28 1.02 0.98 509.47| | 8: 1.87 - 1.79 2789 144 0.93 12.61 1.00 0.98 509.47| | 9: 1.79 - 1.72 2745 138 0.94 10.03 0.98 0.97 288.24| | 10: 1.72 - 1.66 2831 160 0.94 11.07 0.98 0.97 243.93| | 11: 1.66 - 1.61 2712 147 0.93 11.71 0.98 0.97 233.74| | 12: 1.61 - 1.56 2773 144 0.95 8.90 0.99 0.97 137.67| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.03 0.97 137.67| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 123.51| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.98 97.56| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.56| | 17: 1.42 - 1.39 2785 139 0.95 10.88 1.01 0.98 88.84| | 18: 1.39 - 1.36 2741 179 0.94 11.49 1.01 0.98 83.79| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.98 83.79| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 79.82| | 21: 1.32 - 1.30 2785 112 0.94 13.03 0.98 0.96 79.54| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 79.95| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 82.06| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.96 0.95 82.06| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 84.10| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.03 0.93 86.36| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.36| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 90.17| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.60| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.93 91.60| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.54 max = 5911.84 mean = 907.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.45| |phase err.(test): min = 0.00 max = 89.81 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1137 0.1288 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1464 0.1463 0.1496 n_refl.: 87580 remove outliers: r(all,work,free)=0.1464 0.1463 0.1496 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1463 0.1463 0.1495 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1288 n_refl.: 87580 remove outliers: r(all,work,free)=0.1141 0.1134 0.1288 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3927 293.541 247.799 0.430 1.000 0.291 11.894-9.307 93.14 91 4 0.2462 473.362 454.069 0.842 1.002 0.270 9.237-7.194 97.73 208 7 0.2374 387.802 380.460 0.921 1.002 0.159 7.162-5.571 100.00 427 22 0.2166 296.614 285.742 0.907 1.002 0.137 5.546-4.326 100.00 867 58 0.1148 407.177 402.575 0.964 1.002 0.125 4.315-3.360 100.00 1859 96 0.0920 387.229 385.355 1.005 1.002 0.120 3.356-2.611 100.00 3867 181 0.1108 254.389 252.709 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0912 168.637 168.081 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.353 82.730 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.519 36.128 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 23.009 21.551 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0100 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2611 0.1963 0.083 5.357 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_weight: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1231 0.1471 0.006 0.849 9.1 119.5 20.1 258 0.136 1_adp: 0.1237 0.1469 0.006 0.849 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1239 0.1473 0.006 0.849 9.1 119.5 20.1 258 0.136 1_occ: 0.1232 0.1467 0.006 0.849 9.1 119.5 20.1 258 0.136 2_bss: 0.1232 0.1459 0.006 0.849 9.1 119.5 20.1 258 0.136 2_settarget: 0.1232 0.1459 0.006 0.849 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1232 0.1459 0.006 0.867 9.1 119.5 20.1 258 0.136 2_nqh: 0.1233 0.1459 0.006 0.867 9.1 119.5 20.1 258 0.139 2_sol: 0.1204 0.1404 0.006 0.867 9.1 115.0 22.2 419 n/a 2_weight: 0.1204 0.1404 0.006 0.867 9.1 115.0 22.2 419 n/a 2_xyzrec: 0.1189 0.1410 0.007 0.887 9.1 115.0 22.2 419 n/a 2_adp: 0.1189 0.1410 0.007 0.887 9.1 115.0 22.2 419 n/a 2_regHadp: 0.1189 0.1410 0.007 0.887 9.1 115.0 22.2 419 n/a 2_occ: 0.1189 0.1410 0.007 0.887 9.1 115.0 22.2 419 n/a 3_bss: 0.1185 0.1402 0.007 0.887 9.1 115.0 22.2 419 n/a 3_settarget: 0.1185 0.1402 0.007 0.887 9.1 115.0 22.2 419 n/a 3_updatecdl: 0.1185 0.1402 0.007 0.887 9.1 115.0 22.2 419 n/a 3_nqh: 0.1185 0.1402 0.007 0.887 9.1 115.0 22.2 419 n/a 3_sol: 0.1206 0.1403 0.007 0.887 9.1 115.0 21.1 431 n/a 3_weight: 0.1206 0.1403 0.007 0.887 9.1 115.0 21.1 431 n/a 3_xyzrec: 0.1166 0.1330 0.006 0.971 9.1 115.0 21.1 431 n/a 3_adp: 0.1166 0.1330 0.006 0.971 9.1 115.0 21.1 431 n/a 3_regHadp: 0.1166 0.1330 0.006 0.971 9.1 115.0 21.1 431 n/a 3_occ: 0.1156 0.1336 0.006 0.971 9.1 115.0 21.1 431 n/a 4_bss: 0.1148 0.1331 0.006 0.971 9.1 115.0 21.1 431 n/a 4_settarget: 0.1148 0.1331 0.006 0.971 9.1 115.0 21.1 431 n/a 4_updatecdl: 0.1148 0.1331 0.006 0.971 9.1 115.0 21.1 431 n/a 4_nqh: 0.1148 0.1331 0.006 0.971 9.1 115.0 21.1 431 n/a 4_sol: 0.1150 0.1291 0.006 0.971 9.1 115.0 21.0 440 n/a 4_weight: 0.1150 0.1291 0.006 0.971 9.1 115.0 21.0 440 n/a 4_xyzrec: 0.1143 0.1290 0.007 1.058 9.1 115.0 21.0 440 n/a 4_adp: 0.1143 0.1290 0.007 1.058 9.1 115.0 21.0 440 n/a 4_regHadp: 0.1143 0.1290 0.007 1.058 9.1 115.0 21.0 440 n/a 4_occ: 0.1138 0.1287 0.007 1.058 9.1 115.0 21.0 440 n/a 5_bss: 0.1137 0.1290 0.007 1.058 9.1 115.0 21.0 440 n/a 5_settarget: 0.1137 0.1290 0.007 1.058 9.1 115.0 21.0 440 n/a 5_updatecdl: 0.1137 0.1290 0.007 1.061 9.1 115.0 21.0 440 n/a 5_setrh: 0.1138 0.1290 0.007 1.061 9.1 115.0 21.0 440 n/a 5_nqh: 0.1138 0.1290 0.007 1.061 9.1 115.0 21.0 440 n/a 5_sol: 0.1141 0.1289 0.007 1.061 9.1 115.0 21.1 454 n/a 5_weight: 0.1141 0.1289 0.007 1.061 9.1 115.0 21.1 454 n/a 5_xyzrec: 0.1139 0.1289 0.008 1.114 9.1 115.0 21.1 454 n/a 5_adp: 0.1139 0.1289 0.008 1.114 9.1 115.0 21.1 454 n/a 5_regHadp: 0.1139 0.1289 0.008 1.114 9.1 115.0 21.1 454 n/a 5_occ: 0.1137 0.1288 0.008 1.114 9.1 115.0 21.1 454 n/a end: 0.1134 0.1288 0.008 1.114 9.1 115.0 21.1 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2780949_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2780949_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3900 Refinement macro-cycles (run) : 14218.9700 Write final files (write_after_run_outputs) : 72.8900 Total : 14295.2500 Total CPU time: 3.98 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:17:49 PST -0800 (1735366669.02 s) Start R-work = 0.1644, R-free = 0.1774 Final R-work = 0.1134, R-free = 0.1288 =============================================================================== Job complete usr+sys time: 14435.76 seconds wall clock time: 261 minutes 19.06 seconds (15679.06 seconds total)